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Magnesium in PDB 5qj5: Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Z44592329

Enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Z44592329

All present enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Z44592329:
2.7.7.96; 3.6.1.13; 3.6.1.58;

Protein crystallography data

The structure of Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Z44592329, PDB code: 5qj5 was solved by Y.Dubianok, P.Collins, T.Krojer, N.Wright, C.Strain-Damerell, N.Burgess-Brown, C.Bountra, C.H.Arrowsmith, A.Edwards, K.Huber, F.Von Delft, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 78.34 / 1.72
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 49.146, 59.774, 80.086, 79.47, 81.89, 75.78
R / Rfree (%) 21.5 / 25.3

Other elements in 5qj5:

The structure of Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Z44592329 also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Z44592329 (pdb code 5qj5). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Z44592329, PDB code: 5qj5:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5qj5

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Magnesium binding site 1 out of 8 in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Z44592329


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Z44592329 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:35.9
occ:1.00
 OE2 A:GLU116 2.1 31.6 1.0
O A:ALA96 2.1 28.9 1.0
O A:HOH438 2.1 28.1 1.0
O A:HOH418 2.2 28.2 1.0
O A:HOH451 2.2 27.4 1.0
O A:HOH410 2.2 32.5 1.0
CD A:GLU116 3.1 30.1 1.0
C A:ALA96 3.2 26.5 1.0
MG A:MG302 3.3 53.0 1.0
OE1 A:GLU116 3.4 31.1 1.0
OE2 A:GLU166 4.1 77.2 1.0
OE2 A:GLU112 4.1 34.7 1.0
N A:GLY97 4.1 26.2 1.0
N A:ALA96 4.2 22.6 1.0
CA A:ALA96 4.2 22.9 1.0
CA A:GLY97 4.2 25.9 1.0
O A:HOH422 4.2 21.2 1.0
NH2 A:ARG84 4.2 26.0 1.0
NE2 A:GLN82 4.2 31.6 1.0
O A:HOH462 4.3 34.4 0.5
OE1 A:GLN82 4.4 28.8 1.0
O A:HOH456 4.4 43.0 1.0
CG A:GLU116 4.5 29.4 1.0
O A:HOH464 4.6 53.1 1.0
CB A:ALA96 4.6 22.9 1.0
CD A:GLN82 4.7 37.3 1.0
CD A:GLU112 4.9 35.9 1.0

Magnesium binding site 2 out of 8 in 5qj5

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Magnesium binding site 2 out of 8 in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Z44592329


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Z44592329 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:53.0
occ:1.00
 O A:HOH411 1.9 43.2 1.0
OE2 A:GLU112 2.1 34.7 1.0
O A:HOH438 2.1 28.1 1.0
OE2 A:GLU166 2.3 77.2 1.0
OE2 A:GLU116 2.5 31.6 1.0
O A:HOH432 2.7 50.3 1.0
CD A:GLU112 3.1 35.9 1.0
CD A:GLU166 3.2 82.8 1.0
MG A:MG301 3.3 35.9 1.0
CD A:GLU116 3.4 30.1 1.0
OE1 A:GLU112 3.4 36.3 1.0
OE1 A:GLU166 3.5 72.1 1.0
CG A:GLU116 3.6 29.4 1.0
O A:HOH410 3.8 32.5 1.0
O A:ALA96 3.9 28.9 1.0
OE2 A:GLU115 4.2 38.6 1.0
O A:HOH456 4.3 43.0 1.0
OE1 A:GLU116 4.5 31.1 1.0
CG A:GLU112 4.5 31.1 1.0
CG A:GLU166 4.5 72.5 1.0
CB A:GLU112 4.8 28.4 1.0
CA A:GLY97 4.8 25.9 1.0
C A:ALA96 4.9 26.5 1.0
O A:HOH405 4.9 51.2 1.0

Magnesium binding site 3 out of 8 in 5qj5

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Magnesium binding site 3 out of 8 in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Z44592329


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Z44592329 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:35.8
occ:1.00
 OE2 B:GLU116 1.9 38.8 1.0
O B:HOH419 2.0 40.1 1.0
O B:ALA96 2.0 30.8 1.0
O B:HOH406 2.1 32.9 1.0
O B:HOH444 2.2 35.4 1.0
CD B:GLU116 3.0 38.8 1.0
C B:ALA96 3.2 26.9 1.0
MG B:MG303 3.2 59.0 1.0
OE1 B:GLU116 3.3 37.9 1.0
OE2 B:GLU166 3.7 65.4 1.0
O B:HOH465 3.9 32.5 0.5
N B:GLY97 4.1 29.0 1.0
CA B:GLY97 4.1 31.3 1.0
O B:HOH426 4.2 33.5 1.0
N B:ALA96 4.2 26.0 1.0
OE2 B:GLU112 4.2 43.6 1.0
CA B:ALA96 4.2 25.5 1.0
NH2 B:ARG84 4.3 34.5 1.0
CG B:GLU116 4.3 35.2 1.0
NE2 B:GLN82 4.3 34.7 1.0
OE1 B:GLN82 4.4 37.8 1.0
O B:HOH456 4.4 34.5 0.5
CB B:ALA96 4.7 27.6 1.0
CD B:GLN82 4.8 41.6 1.0
O B:HOH459 4.9 46.2 1.0
CD B:GLU166 4.9 75.5 1.0

Magnesium binding site 4 out of 8 in 5qj5

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Magnesium binding site 4 out of 8 in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Z44592329


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Z44592329 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg303

b:59.0
occ:1.00
 OE2 B:GLU112 1.9 43.6 1.0
O B:HOH412 2.0 66.2 1.0
OE2 B:GLU116 2.3 38.8 1.0
O B:HOH444 2.3 35.4 1.0
OE2 B:GLU166 2.4 65.4 1.0
O B:HOH459 2.4 46.2 1.0
CD B:GLU112 3.0 40.8 1.0
CD B:GLU116 3.1 38.8 1.0
MG B:MG302 3.2 35.8 1.0
CG B:GLU116 3.3 35.2 1.0
OE1 B:GLU112 3.4 39.7 1.0
CD B:GLU166 3.4 75.5 1.0
O B:ALA96 3.6 30.8 1.0
OE1 B:GLU166 3.8 82.9 1.0
OE2 B:GLU115 4.0 56.1 1.0
O B:HOH419 4.1 40.1 1.0
OE1 B:GLU116 4.2 37.9 1.0
CG B:GLU112 4.2 38.6 1.0
O B:HOH456 4.4 34.5 0.5
C B:ALA96 4.5 26.9 1.0
CA B:GLY97 4.5 31.3 1.0
CB B:GLU112 4.6 38.7 1.0
CG B:GLU166 4.7 69.8 1.0
O B:HOH406 4.8 32.9 1.0
N B:GLY97 4.8 29.0 1.0
CB B:GLU116 4.8 35.2 1.0
CA B:GLU112 4.9 33.2 1.0
O B:GLU112 5.0 36.7 1.0

Magnesium binding site 5 out of 8 in 5qj5

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Magnesium binding site 5 out of 8 in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Z44592329


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Z44592329 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:62.3
occ:1.00
 O C:HOH441 1.7 49.4 1.0
O C:HOH402 1.9 48.7 1.0
OE2 C:GLU112 2.3 40.1 1.0
OE2 C:GLU116 2.6 37.4 1.0
OE2 C:GLU166 2.6 64.9 1.0
MG C:MG303 2.8 42.3 1.0
CD C:GLU112 3.2 47.9 1.0
OE1 C:GLU112 3.3 58.7 1.0
CD C:GLU166 3.4 73.9 1.0
O C:ALA96 3.4 32.2 1.0
OE1 C:GLU166 3.5 74.0 1.0
O C:HOH460 3.6 58.9 1.0
CD C:GLU116 3.7 36.9 1.0
O C:HOH416 3.8 41.0 1.0
O C:HOH403 4.1 53.4 1.0
O C:HOH449 4.1 33.3 1.0
CA C:GLY97 4.2 39.9 1.0
CG C:GLU116 4.2 33.0 1.0
C C:ALA96 4.4 36.1 1.0
CG C:GLU112 4.5 40.3 1.0
CG C:GLU166 4.7 67.9 1.0
OE1 C:GLU116 4.7 45.6 1.0
N C:GLY97 4.8 30.6 1.0
OE2 C:GLU115 4.8 43.1 1.0
O C:HOH440 4.8 33.8 1.0

Magnesium binding site 6 out of 8 in 5qj5

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Magnesium binding site 6 out of 8 in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Z44592329


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Z44592329 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg303

b:42.3
occ:1.00
 OE2 C:GLU116 1.9 37.4 1.0
O C:HOH441 2.0 49.4 1.0
O C:HOH449 2.0 33.3 1.0
O C:HOH440 2.2 33.8 1.0
O C:ALA96 2.2 32.2 1.0
O C:HOH416 2.3 41.0 1.0
MG C:MG302 2.8 62.3 1.0
CD C:GLU116 3.1 36.9 1.0
C C:ALA96 3.4 36.1 1.0
OE1 C:GLU116 3.4 45.6 1.0
OE2 C:GLU166 3.5 64.9 1.0
O C:HOH402 3.9 48.7 1.0
N C:ALA96 4.1 28.5 1.0
OE2 C:GLU112 4.2 40.1 1.0
CA C:ALA96 4.3 28.2 1.0
N C:GLY97 4.3 30.6 1.0
CA C:GLY97 4.3 39.9 1.0
CG C:GLU116 4.4 33.0 1.0
O C:HOH410 4.4 22.9 0.7
NE2 C:GLN82 4.5 41.5 1.0
OE1 C:GLN82 4.5 34.4 1.0
NH2 C:ARG84 4.5 34.8 1.0
CD C:GLU166 4.7 73.9 1.0
CB C:ALA96 4.7 31.3 1.0
CD C:GLN82 4.9 50.3 1.0
CD C:GLU112 5.0 47.9 1.0

Magnesium binding site 7 out of 8 in 5qj5

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Magnesium binding site 7 out of 8 in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Z44592329


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Z44592329 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg301

b:43.7
occ:1.00
 O D:HOH411 2.0 33.7 1.0
OE2 D:GLU116 2.0 38.3 1.0
O D:HOH403 2.0 31.3 1.0
MG D:MG302 2.3 41.8 1.0
O D:ALA96 2.5 38.4 1.0
O D:HOH431 2.8 51.1 1.0
CD D:GLU116 3.0 47.4 1.0
OE1 D:GLU116 3.4 42.8 1.0
C D:ALA96 3.7 39.7 1.0
OE2 D:GLU166 3.7 89.3 1.0
OE2 D:GLU112 3.9 53.2 1.0
NE2 D:GLN82 4.0 40.8 1.0
O D:HOH401 4.1 48.7 1.0
OE1 D:GLN82 4.3 43.6 1.0
NH2 D:ARG84 4.3 37.1 1.0
N D:ALA96 4.3 34.2 1.0
CG D:GLU116 4.3 42.5 1.0
CA D:ALA96 4.5 35.7 1.0
CD D:GLN82 4.6 50.9 1.0
CA D:GLY97 4.6 41.7 1.0
N D:GLY97 4.6 40.2 1.0
O D:HOH427 4.6 53.1 1.0
CD D:GLU166 4.8 97.3 1.0
CD D:GLU112 4.9 59.6 1.0
CB D:ALA96 5.0 37.8 1.0
CG D:GLU112 5.0 60.8 1.0

Magnesium binding site 8 out of 8 in 5qj5

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Magnesium binding site 8 out of 8 in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Z44592329


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Z44592329 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg302

b:41.8
occ:1.00
 O D:HOH431 2.0 51.1 1.0
OE2 D:GLU112 2.2 53.2 1.0
MG D:MG301 2.3 43.7 1.0
O D:HOH427 2.5 53.1 1.0
OE2 D:GLU166 2.6 89.3 1.0
OE2 D:GLU116 2.8 38.3 1.0
O D:HOH401 2.9 48.7 1.0
O D:ALA96 3.0 38.4 1.0
O D:HOH411 3.1 33.7 1.0
CD D:GLU112 3.4 59.6 1.0
CA D:GLY97 3.6 41.7 1.0
CD D:GLU166 3.9 97.3 1.0
CD D:GLU116 4.0 47.4 1.0
C D:ALA96 4.0 39.7 1.0
CG D:GLU112 4.1 60.8 1.0
OE1 D:GLU112 4.2 50.7 1.0
O D:HOH403 4.2 31.3 1.0
N D:GLY97 4.3 40.2 1.0
OE1 D:GLU166 4.5 0.5 1.0
CG D:GLU116 4.7 42.5 1.0
OE1 D:GLU116 4.8 42.8 1.0
C D:GLY97 4.9 41.6 1.0
CG D:GLU166 5.0 81.4 1.0
N D:LEU98 5.0 40.3 1.0

Reference:

Y.Dubianok, P.Collins, T.Krojer, N.Wright, C.Strain-Damerell, N.Burgess-Brown, C.Bountra, C.H.Arrowsmith, A.Edwards, K.Huber, F.Von Delft. Pandda Analysis Group Deposition To Be Published.
Page generated: Mon Sep 30 02:11:14 2024

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